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- PDB-4wu2: Structure of the PTP-like myo-inositol phosphatase from Selenomon... -

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Basic information

Entry
Database: PDB / ID: 4wu2
TitleStructure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate
ComponentsMyo-inositol phosphohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like ...Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / PHOSPHATE ION / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBruder, L.M. / Mosimann, S.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Foundation for Innovation Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: To Be Published
Title: Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate
Authors: Bruder, L.M.
#1: Journal: J. Biol. Chem. / Year: 2012
Title: Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases.
Authors: Gruninger, R.J. / Dobing, S. / Smith, A.D. / Bruder, L.M. / Selinger, L.B. / Wieden, H.J. / Mosimann, S.C.
#2: Journal: FEBS J. / Year: 2008
Title: Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr.
Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
#3: Journal: Protein Sci. / Year: 2007
Title: Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase.
Authors: Puhl, A.A. / Gruninger, R.J. / Greiner, R. / Janzen, T.W. / Mosimann, S.C. / Selinger, L.B.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myo-inositol phosphohydrolase
B: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,69411
Polymers78,2602
Non-polymers1,4349
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-26 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 137.670, 80.010
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myo-inositol phosphohydrolase


Mass: 39130.000 Da / Num. of mol.: 2 / Fragment: UNP residues 28-346 / Mutation: C252S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7WUJ1, 3-phytase

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Non-polymers , 5 types, 493 molecules

#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: PEG 8000, sodium acetate, sodium chloride, beta-mercapto ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.908
11-H, -K, H+L20.092
ReflectionResolution: 2→44.9 Å / Num. obs: 65377 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.2
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.1data reduction
Aimless0.1.27data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMJ

3mmj


Resolution: 2.15→44.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.931 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21947 2154 4.1 %RANDOM
Rwork0.19677 ---
obs0.19768 50511 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.039 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å2-0 Å20.48 Å2
2---0.82 Å2-0 Å2
3---2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 83 484 5663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195368
X-RAY DIFFRACTIONr_bond_other_d00.024954
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9497284
X-RAY DIFFRACTIONr_angle_other_deg0.62311392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7122.721272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.215874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6851548
X-RAY DIFFRACTIONr_chiral_restr0.0590.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216028
X-RAY DIFFRACTIONr_gen_planes_other00.021332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0272.7522522
X-RAY DIFFRACTIONr_mcbond_other3.0232.752521
X-RAY DIFFRACTIONr_mcangle_it4.54.1183156
X-RAY DIFFRACTIONr_mcangle_other4.5014.123157
X-RAY DIFFRACTIONr_scbond_it4.1123.2282846
X-RAY DIFFRACTIONr_scbond_other4.1123.2282846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2924.6384129
X-RAY DIFFRACTIONr_long_range_B_refined9.33926.86727615
X-RAY DIFFRACTIONr_long_range_B_other9.32626.81327410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 171 -
Rwork0.294 3744 -
obs--99.97 %

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